Abstract:
:AR9 is a giant Bacillus subtilis phage whose uracil-containing double-stranded DNA genome encodes distant homologs of β and β' subunits of bacterial RNA polymerase (RNAP). The products of these genes are thought to assemble into two non-canonical multisubunit RNAPs - a virion RNAP (vRNAP) that is injected into the host along with phage DNA to transcribe early phage genes, and a non-virion RNAP (nvRNAP), which is synthesized during the infection and transcribes late phage genes. We purified the AR9 nvRNAP from infected B. subtilis cells and characterized its transcription activity in vitro. The AR9 nvRNAP requires uracils rather than thymines at specific conserved positions of late viral promoters. Uniquely, the nvRNAP recognizes the template strand of its promoters and is capable of specific initiation of transcription from both double- and single-stranded DNA. While the AR9 nvRNAP does not contain homologs of bacterial RNAP α subunits, it contains, in addition to the β and β'-like subunits, a phage protein gp226. The AR9 nvRNAP lacking gp226 is catalytically active but unable to bind to promoter DNA. Thus, gp226 is required for promoter recognition by the AR9 nvRNAP and may represent a new group of transcription initiation factors.
journal_name
Nucleic Acids Resjournal_title
Nucleic acids researchauthors
Sokolova M,Borukhov S,Lavysh D,Artamonova T,Khodorkovskii M,Severinov Kdoi
10.1093/nar/gkx264subject
Has Abstractpub_date
2017-06-02 00:00:00pages
5958-5967issue
10eissn
0305-1048issn
1362-4962pii
3603318journal_volume
45pub_type
杂志文章abstract::The unknown modified nucleotide G*, isolated from both Schizosaccharomyces pombe and Torulopsis utilis initiator tRNAs(Met), has been identified as an O-ribosyl-(1"----2')-guanosine-5"-phosphate, called Gr(p), by means of HPLC, UV-absorption, mass spectrometry and periodate oxidation procedures. By comparison with the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/19.19.5199
更新日期:1991-10-11 00:00:00
abstract::The genomic distribution of 23 nuclear genes from three dicotyledons (pea, sunflower, tobacco) and five monocotyledons of the Gramineae family (barley, maize, rice, oat, wheat) was studied by localizing these genes in DNA fractions obtained by preparative centrifugation in Cs2SO4/BAMD density gradients. Each one of th...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.7.1859
更新日期:1990-04-11 00:00:00
abstract::Traditional Chinese medicine (TCM) is not only an effective solution for primary health care, but also a great resource for drug innovation and discovery. To meet the increasing needs for TCM-related data resources, we developed ETCM, an Encyclopedia of Traditional Chinese Medicine. ETCM includes comprehensive and sta...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gky987
更新日期:2019-01-08 00:00:00
abstract::Exposure to genotoxic agents, such as ionizing radiation (IR), produces double-strand breaks, repaired predominantly in mammalian cells by non-homologous end-joining (NHEJ). Ku70 was identified as an interacting partner of a proteolytic Cyclin E (CycE) fragment, p18CycE. p18CycE endogenous generation during IR-induced...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt812
更新日期:2013-12-01 00:00:00
abstract::Adaptation of the P1 phage-derived Cre /loxP site- specific recombination system to the gene targeting technique allows for the conditional deletion of genes in mice. To selectively modify genes in B lymphocytes, we have generated mice (designated CD19-Cre) which express cre under the transcriptional control of the B ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/25.6.1317
更新日期:1997-03-15 00:00:00
abstract::The open state of human topoisomerase I has been probed by molecular dynamics simulation, starting from the coordinates of the closed structure of the protein complexed with DNA, after elimination of the 22-bp DNA duplex oligonucleotide. A repulsion force between the two lips of the protein has been introduced for a s...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm199
更新日期:2007-01-01 00:00:00
abstract::Stabilization of stalled replication forks prevents excessive fork reversal or degradation, which can undermine genome integrity. The WRN protein is unique among the other human RecQ family members to possess exonuclease activity. However, the biological role of the WRN exonuclease is poorly defined. Recently, the WRN...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz431
更新日期:2019-07-26 00:00:00
abstract::We show herein the transcription of a processed gene that originated from a spliced transcript. Recently, we isolated the human and murine homologues of the yeast chromatin protein, SPT4. The Supt4h gene is spliced normally from five exons encoded by chromosome 11. Here we show that a related sequence on chromosome 10...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/26.21.4960
更新日期:1998-11-01 00:00:00
abstract::The promoter of the human BCR gene, regulating the transcription of the chimeric BCR/ABL mRNA in leukemia, has been isolated and characterized. A region of 1.1 kb immediately 5' to the transcription start site was analyzed in detail by sequencing, DNase 1 footprinting, gel retardation and functional studies. These exp...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/18.23.7119
更新日期:1990-12-11 00:00:00
abstract::Next-generation sequencing allows now the sequencing of small RNA molecules and the estimation of their expression levels. Consequently, there will be a high demand of bioinformatics tools to cope with the several gigabytes of sequence data generated in each single deep-sequencing experiment. Given this scene, we deve...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkp347
更新日期:2009-07-01 00:00:00
abstract::Protein structures are an ensemble of atoms determined experimentally mostly by X-ray crystallography or Nuclear Magnetic Resonance. Studying 3D protein structures is a key point for better understanding protein function at a molecular level. We propose a set of accurate tools, for analysing protein structures, based ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkt509
更新日期:2013-07-01 00:00:00
abstract::Mechanisms that preserve genome integrity are highly important during the normal life cycle of human cells. Loss of genome protective mechanisms can lead to the development of diseases such as cancer. Checkpoint kinases function in the cellular surveillance pathways that help cells to cope with DNA damage. Importantly...
journal_title:Nucleic acids research
pub_type: 杂志文章,评审
doi:10.1093/nar/gkr697
更新日期:2012-01-01 00:00:00
abstract::ADGO 2.0 is a web-based tool that provides composite interpretations for microarray data comparing two sample groups as well as lists of genes from diverse sources of biological information. Some other tools also incorporate composite annotations solely for interpreting lists of genes but usually provide highly redund...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr392
更新日期:2011-07-01 00:00:00
abstract::The efficiency of Nucleotide Excision Repair (NER)process is crucial for maintaining genomic integrity because in many organisms, including humans, it represents the only system able to repair a wide range of DNA damage. The aim of the work was to investigate whether the efficiency of the repair of photoproducts induc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkv081
更新日期:2015-02-27 00:00:00
abstract::A feature of Haemophilus influenzae genomes is the presence of several loci containing tracts of six or more identical tetranucleotide repeat units. These repeat tracts are unstable and mediate high frequency, reversible alterations in the expression of surface antigens. This process, termed phase variation (PV), enab...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gki180
更新日期:2005-01-14 00:00:00
abstract::The nucleotide sequence of the faeD gene of Escherichia coli and the amino acid sequence of its product is presented. The faeD product is an outer membrane protein required for transport of K88ab fimbrial subunits across the outer membrane. The protein is synthesized as a precursor containing a signal peptide, and the...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/14.6.2443
更新日期:1986-03-25 00:00:00
abstract::The cDNA encoding Chinese hamster O6-alkylguanine-DNA-alkyltransferase (ATase) has been isolated from a library prepared from RNA isolated from V79 lung fibroblasts which had an upregulated level of this repair activity following stepwise selection with a chloroethylating agent (1, 2). Expression of the cDNA in E. col...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/20.8.1891
更新日期:1992-04-25 00:00:00
abstract::A U3 snoRNA gene isolated from a Chlamydomonas reinhardtii (CRE:) genomic library contains putative pol III-specific transcription signals similar to those of RNA polymerase III-specific small nuclear (sn)RNA genes of higher plants. The 222 nt long CRE: U3 snoRNA was immunoprecipitated by anti-gamma-mpppN antisera, bu...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.15.2959
更新日期:2000-08-01 00:00:00
abstract::The representational difference analysis (RDA) and other subtraction techniques are used to enrich sample-specific sequences by elimination of ubiquitous sequences existing in both the sample of interest (tester) and the subtraction partner (driver). While applying the RDA to genomic DNA of cutaneous lymphoma cells in...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.4.e20
更新日期:2001-02-15 00:00:00
abstract::The ciliate Tetrahymena thermophila is an important eukaryotic model organism that has been used in pioneering studies of general phenomena, such as ribozymes, telomeres, chromatin structure and genome reorganization. Recent work has shown that Tetrahymena has many classes of small RNA molecules expressed during veget...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkr792
更新日期:2012-02-01 00:00:00
abstract::High-resolution structures of proteins remain the most valuable source for understanding their function in the cell and provide leads for drug design. Since the availability of sufficient protein structures to tackle complex problems such as modeling backbone moves or docking remains a problem, alternative approaches ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq972
更新日期:2011-01-01 00:00:00
abstract::We present the results of in vitro binding studies aimed at defining the key recognition elements on the MS2 RNA translational operator (TR) essential for complex formation with coat protein. We have used chemically synthesized operators carrying modified functional groups at defined nucleotide positions, which are es...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/23.13.2512
更新日期:1995-07-11 00:00:00
abstract::Restriction-free cloning (RF-cloning) is a PCR-based technology that expands on the QuikChange™ mutagenesis process originally popularized by Stratagene in the mid-1990s, and allows the insertion of essentially any sequence into any plasmid at any location. While RF-cloning is a powerful tool for the design of custom ...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gks396
更新日期:2012-07-01 00:00:00
abstract::The modulation of GLI2, an oncogenic transcription factor commonly upregulated in cancer, is in many cases not due to genetic defects, suggesting dysregulation through alternative mechanisms. The identity of these molecular events remains for the most part unknown. Here, we identified TFII-I as a novel repressor of GL...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkaa476
更新日期:2020-07-27 00:00:00
abstract::A 12 bp long GCN4-binding, self-complementary duplex DNA d(CATGACGTCATG)(2) has been investigated by NMR spectroscopy to study the structure and dynamics of the molecule in aqueous solution. The NMR structure of the DNA obtained using simulated annealing and iterative relaxation matrix calculations compares quite clos...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/29.2.499
更新日期:2001-01-15 00:00:00
abstract::When averaged over the full yeast protein-protein interaction and transcriptional regulatory networks, protein hubs with many interaction partners or regulators tend to evolve significantly more slowly due to increased negative selection. However, genome-wide analysis of protein evolution in the subnetworks of associa...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkq353
更新日期:2010-10-01 00:00:00
abstract::Microbial functional diversification is driven by environmental factors, i.e. microorganisms inhabiting the same environmental niche tend to be more functionally similar than those from different environments. In some cases, even closely phylogenetically related microbes differ more across environments than across tax...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkx1060
更新日期:2018-01-04 00:00:00
abstract::Despite much information as to the structure and function of the general transcription factors, little is known about the regulation of their expression. Transcription of the Saccharomyces cerevisiae SUA7 (TFIIB) gene results in the formation of two discrete transcripts. It was originally reported that the two transcr...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/28.22.4435
更新日期:2000-11-15 00:00:00
abstract::Bacterial genomics has revolutionized our understanding of the microbial tree of life; however, mapping and visualizing the distribution of functional traits across bacteria remains a challenge. Here, we introduce AnnoTree-an interactive, functionally annotated bacterial tree of life that integrates taxonomic, phyloge...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkz246
更新日期:2019-05-21 00:00:00
abstract::The widely accepted model for the processing of tRNAs in Escherichia coli involves essential initial cleavages by RNase E within polycistronic transcripts to generate pre-tRNAs that subsequently become substrates for RNase P. However, recently we identified two polycistronic tRNA transcripts whose endonucleolytic proc...
journal_title:Nucleic acids research
pub_type: 杂志文章
doi:10.1093/nar/gkm991
更新日期:2008-02-01 00:00:00